Carbon catabolite repression involves physical interaction of the transcription factor CRE1/CreA and the Tup1–Cyc8 complex in Penicillium oxalicum and Trichoderma reesei

Abstract Background Cellulolytic enzyme production in filamentous fungi requires a release from carbon catabolite repression (CCR). The protein CRE1/CreA (CRE = catabolite responsive element) is a key transcription factor (TF) that is involved in CCR and represses cellulolytic gene expression. CRE1/CreA represents the functional equivalent of Mig1p, an important Saccharomyces cerevisiae TF in CCR that exerts its repressive effect by recruiting a corepressor complex Tup1p–Cyc8p. Although it is known from S. cerevisiae that CRE1/CreA might repress gene expression via interacting with the corepressor complex Tup1–Cyc8, this mechanism is unconfirmed in other filamentous fungi, since the physical interaction has not yet been verified in these organisms. The precise mechanism on how CRE1/CreA achieves transcriptional repression after DNA binding remains unknown. Results The results from tandem affinity purification and bimolecular fluorescence complementation revealed a direct physical interaction between the TF CRE1/CreA and the complex Tup1–Cyc8 in the nucleus of cellulolytic fungus Trichoderma reesei and Penicillium oxalicum. Both fungi have the ability to secrete a complex arsenal of enzymes to synergistically degrade lignocellulosic materials. In P. oxalicum, the protein PoCyc8, a subunit of complex Tup1–Cyc8, interacts directly with TF PoCreA and histone H3 lysine 36 (H3K36) methyltransferase PoSet2 in the nucleus. The di-methylation level of H3K36 in the promoter of prominent cellulolytic genes (cellobiohydrolase-encoding gene Pocbh1/cel7A and endoglucanase-encoding gene Poegl1/cel7B) is positively correlated with the expression levels of TF PoCreA. Since the methylation of H3K36 was also demonstrated to be a repression marker of cellulolytic gene expression, it appears feasible that the cellulolytic genes are repressed via PoCreA-Tup1–Cyc8-Set2-mediated transcriptional repression. Conclusion This study verifies the long-standing conjecture that the TF CRE1/CreA represses gene expression by interacting with the corepressor complex Tup1–Cyc8 in filamentous fungi. A reasonable explanation is proposed that PoCreA represses gene expression by recruiting complex PoTup1–Cyc8. Histone methyltransferase Set2, which methylates H3K36, is also involved in the regulatory network by interacting with PoCyc8. The findings contribute to the understanding of CCR mechanism in filamentous fungi and could aid in biotechnologically relevant enzyme production.

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Ethanolamine Utilization and Bacterial Microcompartment Formation Are Subject to Carbon Catabolite Repression

Journal of Bacteriology ◽

10.1128/jb.00703-18 ◽

2019 ◽

Vol 201 (10) ◽

Cited By ~ 2

Author(s):

Karan Gautam Kaval ◽

Margo Gebbie ◽

Jonathan R. Goodson ◽

Melissa R. Cruz ◽

Wade C. Winkler ◽

...

Keyword(s):

Gene Expression ◽

Enterococcus Faecalis ◽

Small Rna ◽

Catabolite Repression ◽

Carbon Catabolite Repression ◽

Bioinformatics Analysis ◽

Maximum Efficiency ◽

Gi Tract ◽

Content Type ◽

Regulatory Factors

ABSTRACT Ethanolamine (EA) is a compound prevalent in the gastrointestinal (GI) tract that can be used as a carbon, nitrogen, and/or energy source. Enterococcus faecalis, a GI commensal and opportunistic pathogen, contains approximately 20 ethanolamine utilization (eut) genes encoding the necessary regulatory, enzymatic, and structural proteins for this process. Here, using a chemically defined medium, two regulatory factors that affect EA utilization were examined. First, the functional consequences of loss of the small RNA (sRNA) EutX on the efficacy of EA utilization were investigated. One effect observed, as loss of this negative regulator causes an increase in eut gene expression, was a concomitant increase in the number of catabolic bacterial microcompartments (BMCs) formed. However, despite this increase, the growth of the strain was repressed, suggesting that the overall efficacy of EA utilization was negatively affected. Second, utilizing a deletion mutant and a complement, carbon catabolite control protein A (CcpA) was shown to be responsible for the repression of EA utilization in the presence of glucose. A predicted cre site in one of the three EA-inducible promoters, PeutS, was identified as the target of CcpA. However, CcpA was shown to affect the activation of all the promoters indirectly through the two-component system EutV and EutW, whose genes are under the control of the PeutS promoter. Moreover, a bioinformatics analysis of bacteria predicted to contain CcpA and cre sites revealed that a preponderance of BMC-containing operons are likely regulated by carbon catabolite repression (CCR). IMPORTANCE Ethanolamine (EA) is a compound commonly found in the gastrointestinal (GI) tract that can affect the behavior of human pathogens that can sense and utilize it, such as Enterococcus faecalis and Salmonella. Therefore, it is important to understand how the genes that govern EA utilization are regulated. In this work, we investigated two regulatory factors that control this process. One factor, a small RNA (sRNA), is shown to be important for generating the right levels of gene expression for maximum efficiency. The second factor, a transcriptional repressor, is important for preventing expression when other preferred sources of energy are available. Furthermore, a global bioinformatics analysis revealed that this second mechanism of transcriptional regulation likely operates on similar genes in related bacteria.

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Carbon Catabolite Repression Regulates Glyoxylate Cycle Gene Expression in Cucumber.

The Plant Cell ◽

10.1105/tpc.6.5.761 ◽

1994 ◽

pp. 761-772 ◽

Cited By ~ 166

Author(s):

I. A. Graham ◽

K. J. Denby ◽

C. J. Leaver

Keyword(s):

Gene Expression ◽

Catabolite Repression ◽

Carbon Catabolite Repression ◽

Glyoxylate Cycle

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Involvement of carbon catabolite repression on regulation of endopolygalacturonase gene expression in citrus fruit

Journal of General Plant Pathology ◽

10.1007/s10327-002-0020-0 ◽

2003 ◽

Vol 69 (2) ◽

pp. 120-125 ◽

Cited By ~ 8

Author(s):

Kouhei Ohtani ◽

Atsunori Isshiki ◽

Hiroshi Katoh ◽

Hiroyuki Yamamoto ◽

Kazuya Akimitsu

Keyword(s):

Gene Expression ◽

Catabolite Repression ◽

Carbon Catabolite Repression ◽

Citrus Fruit

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Induction and Repression of Hydrolase Genes in Aspergillus oryzae

Frontiers in Microbiology ◽

10.3389/fmicb.2021.677603 ◽

2021 ◽

Vol 12 ◽

Author(s):

Mizuki Tanaka ◽

Katsuya Gomi

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Aspergillus Oryzae ◽

Catabolite Repression ◽

Food Industry ◽

Carbon Catabolite Repression ◽

Proteolytic Enzymes ◽

Current Knowledge ◽

Glycosyl Hydrolase ◽

Fermented Foods

The filamentous fungus Aspergillus oryzae, also known as yellow koji mold, produces high levels of hydrolases such as amylolytic and proteolytic enzymes. This property of producing large amounts of hydrolases is one of the reasons why A. oryzae has been used in the production of traditional Japanese fermented foods and beverages. A wide variety of hydrolases produced by A. oryzae have been used in the food industry. The expression of hydrolase genes is induced by the presence of certain substrates, and various transcription factors that regulate such expression have been identified. In contrast, in the presence of glucose, the expression of the glycosyl hydrolase gene is generally repressed by carbon catabolite repression (CCR), which is mediated by the transcription factor CreA and ubiquitination/deubiquitination factors. In this review, we present the current knowledge on the regulation of hydrolase gene expression, including CCR, in A. oryzae.

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Regulation of Arabinose and Xylose Metabolism in Escherichia coli

Applied and Environmental Microbiology ◽

10.1128/aem.01970-09 ◽

2009 ◽

Vol 76 (5) ◽

pp. 1524-1532 ◽

Cited By ~ 94

Author(s):

Tasha A. Desai ◽

Christopher V. Rao

Keyword(s):

Gene Expression ◽

Escherichia Coli ◽

Catabolite Repression ◽

Carbon Catabolite Repression ◽

Plant Biomass ◽

Xylose Metabolism ◽

Sugar Utilization ◽

E Coli ◽

Metabolic Genes ◽

Pentose Sugars

ABSTRACT Bacteria such as Escherichia coli will often consume one sugar at a time when fed multiple sugars, in a process known as carbon catabolite repression. The classic example involves glucose and lactose, where E. coli will first consume glucose, and only when it has consumed all of the glucose will it begin to consume lactose. In addition to that of lactose, glucose also represses the consumption of many other sugars, including arabinose and xylose. In this work, we characterized a second hierarchy in E. coli, that between arabinose and xylose. We show that, when grown in a mixture of the two pentoses, E. coli will consume arabinose before it consumes xylose. Consistent with a mechanism involving catabolite repression, the expression of the xylose metabolic genes is repressed in the presence of arabinose. We found that this repression is AraC dependent and involves a mechanism where arabinose-bound AraC binds to the xylose promoters and represses gene expression. Collectively, these results demonstrate that sugar utilization in E. coli involves multiple layers of regulation, where cells will consume first glucose, then arabinose, and finally xylose. These results may be pertinent in the metabolic engineering of E. coli strains capable of producing chemical and biofuels from mixtures of hexose and pentose sugars derived from plant biomass.

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Utilization of Lactose and Galactose by Streptococcus mutans: Transport, Toxicity, and Carbon Catabolite Repression

Journal of Bacteriology ◽

10.1128/jb.01624-09 ◽

2010 ◽

Vol 192 (9) ◽

pp. 2434-2444 ◽

Cited By ~ 61

Author(s):

Lin Zeng ◽

Satarupa Das ◽

Robert A. Burne

Keyword(s):

Gene Expression ◽

Streptococcus Mutans ◽

Catabolite Repression ◽

Dairy Products ◽

Carbon Catabolite Repression ◽

Human Tooth ◽

Tooth Decay ◽

Galactose Metabolism ◽

Promoter Fusion ◽

High Degree

ABSTRACT Abundant in milk and other dairy products, lactose is considered to have an important role in oral microbial ecology and can contribute to caries development in both adults and young children. To better understand the metabolism of lactose and galactose by Streptococcus mutans, the major etiological agent of human tooth decay, a genetic analysis of the tagatose-6-phosphate (lac) and Leloir (gal) pathways was performed in strain UA159. Deletion of each gene in the lac operon caused various alterations in expression of a PlacA -cat promoter fusion and defects in growth on either lactose (lacA, lacB, lacF, lacE, and lacG), galactose (lacA, lacB, lacD, and lacG) or both sugars (lacA, lacB, and lacG). Failure to grow in the presence of galactose or lactose by certain lac mutants appeared to arise from the accumulation of intermediates of galactose metabolism, particularly galatose-6-phosphate. The glucose- and lactose-PTS permeases, EIIMan and EIILac, respectively, were shown to be the only effective transporters of galactose in S. mutans. Furthermore, disruption of manL, encoding EIIABMan, led to increased resistance to glucose-mediated CCR when lactose was used to induce the lac operon, but resulted in reduced lac gene expression in cells growing on galactose. Collectively, the results reveal a remarkably high degree of complexity in the regulation of lactose/galactose catabolism.

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Carbon catabolite repression of xylanase I (xyn1) gene expression in Trichoderma reesei

Molecular Microbiology ◽

10.1046/j.1365-2958.1996.00094.x ◽

1996 ◽

Vol 21 (6) ◽

pp. 1273-1281 ◽

Cited By ~ 121

Author(s):

Robert L. Mach ◽

Joseph Strauss ◽

Susanne Zeilinger ◽

Martin Schindler ◽

Christian P. Kubicek

Keyword(s):

Gene Expression ◽

Trichoderma Reesei ◽

Catabolite Repression ◽

Carbon Catabolite Repression

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Disruption of alpha-tubulin releases carbon catabolite repression and enhances enzyme production in Trichoderma reesei even in the presence of glucose

Biotechnology for Biofuels ◽

10.1186/s13068-021-01887-0 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Nozomu Shibata ◽

Hiroshi Kakeshita ◽

Kazuaki Igarashi ◽

Yasushi Takimura ◽

Yosuke Shida ◽

...

Keyword(s):

Trichoderma Reesei ◽

Catabolite Repression ◽

Enzyme Production ◽

Protein Production ◽

Carbon Catabolite Repression ◽

Transcriptional Regulator ◽

Secretory Protein ◽

Sugar Transporter ◽

Alpha Tubulin ◽

High Enzyme

Abstract Background Trichoderma reesei is a filamentous fungus that is important as an industrial producer of cellulases and hemicellulases due to its high secretion of these enzymes and outstanding performance in industrial fermenters. However, the reduction of enzyme production caused by carbon catabolite repression (CCR) has long been a problem. Disruption of a typical transcriptional regulator, Cre1, does not sufficiently suppress this reduction in the presence of glucose. Results We found that deletion of an α-tubulin (tubB) in T. reesei enhanced both the amount and rate of secretory protein production. Also, the tubulin-disrupted (ΔtubB) strain had high enzyme production and the same enzyme profile even if the strain was cultured in a glucose-containing medium. From transcriptome analysis, the ΔtubB strain exhibited upregulation of both cellulase and hemicellulase genes including some that were not originally induced by cellulose. Moreover, cellobiose transporter genes and the other sugar transporter genes were highly upregulated, and simultaneous uptake of glucose and cellobiose was also observed in the ΔtubB strain. These results suggested that the ΔtubB strain was released from CCR. Conclusion Trichoderma reesei α-tubulin is involved in the transcription of cellulase and hemicellulase genes, as well as in CCR. This is the first report of overcoming CCR by disrupting α-tubulin gene in T. reesei. The disruption of α-tubulin is a promising approach for creating next-generation enzyme-producing strains of T. reesei.

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